-
Notifications
You must be signed in to change notification settings - Fork 8
Expand file tree
/
Copy pathprecon_all_devtable.html
More file actions
549 lines (529 loc) · 42.2 KB
/
Copy pathprecon_all_devtable.html
File metadata and controls
549 lines (529 loc) · 42.2 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>precon_all Dev Table — Process Flow</title>
<style>
:root{
--ink:#1a1a1a; --muted:#6b6b6b; --line:#d9d6cf; --line2:#eceae4;
--paper:#fbfaf7; --band:#2f3b30; --bandink:#f3f1ea;
--cmd:#f4f2ec; --cmdink:#232323;
--fs:#2d6a4f; --fsl:#1d4e89; --ants:#9a3412; --afni:#6b21a8; --wb:#a16207;
--stepbg:#efeee8;
}
*{box-sizing:border-box}
html{-webkit-text-size-adjust:100%}
body{
margin:0; background:var(--paper); color:var(--ink);
font-family:"Iowan Old Style","Palatino Linotype",Palatino,Georgia,serif;
line-height:1.5;
}
.wrap{max-width:1180px; margin:0 auto; padding:40px 22px 90px}
header.masthead{border-bottom:3px double var(--ink); padding-bottom:18px; margin-bottom:26px}
h1{font-size:30px; margin:0 0 4px; letter-spacing:-.01em}
h1 .mono{font-family:ui-monospace,"SF Mono",Menlo,Consolas,monospace; font-size:26px}
.sub{color:var(--muted); font-size:15px; margin:0}
.lede{font-size:15px; max-width:78ch; margin:16px 0 0}
.lede code{font-family:ui-monospace,Menlo,Consolas,monospace; font-size:13px; background:var(--cmd); padding:1px 5px; border-radius:3px}
a{color:var(--fsl); text-decoration:none; border-bottom:1px solid rgba(29,78,137,.3)}
/* legend */
.legend{display:flex; flex-wrap:wrap; gap:8px 16px; align-items:center;
margin:22px 0 8px; padding:12px 14px; background:#fff; border:1px solid var(--line); border-radius:6px}
.legend .ll{font-size:12.5px; color:var(--muted); text-transform:uppercase; letter-spacing:.08em; margin-right:4px}
.tag{display:inline-block; font-family:ui-monospace,Menlo,Consolas,monospace; font-size:11px;
font-weight:700; letter-spacing:.03em; color:#fff; padding:2px 7px; border-radius:4px; vertical-align:middle}
.tag.fs{background:var(--fs)} .tag.fsl{background:var(--fsl)} .tag.ants{background:var(--ants)}
.tag.afni{background:var(--afni)} .tag.wb{background:var(--wb)}
.note{font-size:13px; color:var(--muted); margin:6px 2px 0}
/* module band */
.module{margin-top:40px}
.band{background:var(--band); color:var(--bandink); padding:11px 16px; border-radius:6px 6px 0 0;
font-family:ui-monospace,Menlo,Consolas,monospace; font-size:14px; font-weight:700; letter-spacing:.01em;
display:flex; flex-wrap:wrap; gap:6px 14px; align-items:baseline}
.band .mtitle{font-size:15px}
.band .mdesc{font-family:"Iowan Old Style",Georgia,serif; font-weight:400; font-size:13px; color:#c8d3c4}
table{width:100%; border-collapse:collapse; background:#fff; font-size:13.5px}
thead th{background:var(--stepbg); color:#333; text-align:left; font-weight:700; font-size:11.5px;
text-transform:uppercase; letter-spacing:.07em; padding:8px 12px; border-bottom:2px solid var(--line);
position:sticky; top:0; z-index:2}
th.c-step{width:15%} th.c-in{width:22%} th.c-cmd{width:44%} th.c-out{width:19%}
tbody td{padding:9px 12px; border-bottom:1px solid var(--line2); vertical-align:top}
tbody tr:hover{background:#fcfbf8}
.sub-band td{background:#f6f5f0; border-bottom:1px solid var(--line);
font-family:ui-monospace,Menlo,Consolas,monospace; font-size:12px; font-weight:700; color:#444; letter-spacing:.02em}
.sub-band .loc{float:right; font-weight:400; color:var(--muted)}
.step{font-family:ui-monospace,Menlo,Consolas,monospace; font-size:12px; color:#333; font-weight:600}
.io{font-family:ui-monospace,Menlo,Consolas,monospace; font-size:11.5px; color:#3a3a3a; line-height:1.55}
.io span{display:block; white-space:nowrap; overflow:hidden; text-overflow:ellipsis}
.cmd{font-family:ui-monospace,"SF Mono",Menlo,Consolas,monospace; font-size:11.5px; color:var(--cmdink);
line-height:1.55; white-space:pre-wrap; word-break:break-word}
.cmd b{font-weight:700}
.opt{color:#7a5}
td .tag{margin-bottom:6px}
.muted{color:var(--muted)}
.foot{margin-top:46px; padding-top:16px; border-top:1px solid var(--line); font-size:13px; color:var(--muted)}
.foot code{font-family:ui-monospace,Menlo,Consolas,monospace; font-size:12px}
@media (max-width:760px){
th.c-in,td.c-in{display:none}
th.c-step{width:26%} th.c-cmd{width:52%} th.c-out{width:22%}
.wrap{padding:24px 12px 60px}
}
</style>
</head>
<body>
<div class="wrap">
<header class="masthead">
<h1><span class="mono">precon_all</span> — Process Flow (Dev Table)</h1>
<p class="sub">Preclinical / animal cortical surface reconstruction · driver: <span style="font-family:ui-monospace,Menlo,monospace">surfing_safari.sh</span></p>
<p class="lede">Modeled on FreeSurfer’s <a href="https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable">ReconAllDevTable</a>. Each <strong>module</strong> (<code>-r precon_1 … precon_art</code>) is the analogue of <code>recon-all -autorecon1/2/3</code>; within it, steps run top-to-bottom. Commands are the real invocations from the repo (<code>bin/</code>, <code>bin/group_scripts/</code>, <code>utils/</code>), with the source file and line noted on each step band. Run with <code>surfing_safari.sh -i <T1.nii.gz> -r precon_all -a <animal></code>. <code>?h</code> = lh / rh.</p>
<div class="legend">
<span class="ll">Toolkit</span>
<span><span class="tag fs">FS</span> FreeSurfer</span>
<span><span class="tag fsl">FSL</span> FSL</span>
<span><span class="tag ants">ANTS</span> ANTs</span>
<span><span class="tag afni">AFNI</span> AFNI</span>
<span><span class="tag wb">WB</span> Workbench</span>
</div>
<p class="note">Branch points (either/or) are marked <em>[FNIRT]/[ANTs]</em> for extraction and <em>[FAST]/[Atropos]</em> for segmentation. <code>${ANTSPATH}</code> / <code>$FSLDIR/bin</code> prefixes omitted for readability.</p>
</header>
<!-- ============================ PRECON_1 ============================ -->
<section class="module">
<div class="band">
<span class="mtitle">surfing_safari.sh -r precon_1</span>
<span class="mdesc">Brain extraction only (pipeline step 1). Also the first stage of <code>precon_all</code>.</span>
</div>
<table>
<thead><tr>
<th class="c-step">Step / flag</th><th class="c-in">Input</th><th class="c-cmd">Command line</th><th class="c-out">Output</th>
</tr></thead>
<tbody>
<tr class="sub-band"><td colspan="4">bet_animal.sh — brain extraction (called with <span class="muted">-d y</span> denoise; <span class="muted">-e</span> = ANTs path; <span class="muted">-m</span> = prior <code>pre_extract.mat</code>)<span class="loc">bin/bet_animal.sh</span></td></tr>
<tr>
<td class="step">denoise</td>
<td class="io"><span>${T1}</span></td>
<td class="cmd"><span class="tag ants">ANTS</span><b>DenoiseImage</b> <span class="opt">-d</span> 3 <span class="opt">-i</span> ${T1} <span class="opt">-o</span> sanlm_${T1} <span class="opt">-v</span></td>
<td class="io"><span>sanlm_${T1}</span></td>
</tr>
<tr>
<td class="step">clamp + hdr</td>
<td class="io"><span>sanlm_${T1}</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>fslmaths</b> sanlm_${T1} <span class="opt">-thr</span> 0 sanlm_${T1}
<span class="tag fsl">FSL</span><b>fslorient</b> <span class="opt">-copyqform2sform</span> sanlm_${T1}</td>
<td class="io"><span>sanlm_${T1}</span></td>
</tr>
<tr>
<td class="step">register <span class="muted">[FNIRT]</span></td>
<td class="io"><span>sanlm_${T1}</span><span>${temp} (template)</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>flirt</b> <span class="opt">-in</span> sanlm_${T1} <span class="opt">-ref</span> ${temp} <span class="opt">-dof</span> 12 <span class="opt">-omat</span> transforms/init.mat <span class="opt">-searchrx/ry/rz</span> -180 180 <span class="opt">-out</span> str_2std_linear
<span class="tag fsl">FSL</span><b>fnirt</b> <span class="opt">--in=</span>sanlm_${T1} <span class="opt">--ref=</span>${temp} <span class="opt">--cout=</span>transforms/str2std_warp <span class="opt">-v --aff=</span>transforms/init.mat</td>
<td class="io"><span>transforms/init.mat</span><span>transforms/str2std_warp</span></td>
</tr>
<tr>
<td class="step">invert + mask <span class="muted">[FNIRT]</span></td>
<td class="io"><span>str2std_warp</span><span>${prob_mask}</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>invwarp</b> <span class="opt">--warp=</span>transforms/str2std_warp <span class="opt">--ref=</span>sanlm_${T1} <span class="opt">--out=</span>transforms/std2str_warp
<span class="tag fsl">FSL</span><b>applywarp</b> <span class="opt">--in=</span>${prob_mask} <span class="opt">--ref=</span>sanlm_${T1} <span class="opt">--interp=</span>nn <span class="opt">--warp=</span>transforms/std2str_warp <span class="opt">--out=</span>${T1}_brain_mask
<span class="tag fsl">FSL</span><b>fslmaths</b> sanlm_${T1} <span class="opt">-mas</span> ${T1}_brain_mask ${T1}_brain</td>
<td class="io"><span>std2str_warp</span><span>*_brain_mask</span><span>*_brain</span></td>
</tr>
<tr>
<td class="step">register <span class="muted">[ANTs -e]</span></td>
<td class="io"><span>sanlm_${T1}</span><span>${premat} (opt)</span><span>${prob_mask}</span></td>
<td class="cmd"><span class="tag ants">ANTS</span><b>ImageMath</b> 3 sanlm_${T1} TruncateImageIntensity sanlm_${T1} 0.05 0.999
<span class="tag fs">FS</span><b>lta_convert</b> <span class="opt">--infsl</span> ${premat} <span class="opt">--outitk</span> transforms/pre_extract.txt <span class="opt">--src</span> sanlm_${T1} <span class="opt">--trg</span> ${temp}
<span class="tag ants">ANTS</span><b>ConvertTransformFile</b> 3 pre_extract.txt pre_extract.mat <span class="opt">--convertToAffineType</span>
<span class="tag ants">ANTS</span><b>antsBrainExtraction.sh</b> <span class="opt">-d</span> 3 <span class="opt">-e</span> ${temp} <span class="opt">-a</span> sanlm_${T1} <span class="opt">-m</span> ${prob_mask} <span class="opt">-o</span> ANTs [<span class="opt">-r</span> pre_extract.mat]
<span class="tag ants">ANTS</span><b>antsRegistrationSyN.sh</b> <span class="opt">-d</span> 3 <span class="opt">-f</span> ${temp} <span class="opt">-m</span> sanlm_${T1} <span class="opt">-x</span> std_brain_mask,${T1}_brain_mask <span class="opt">-o</span> transforms/ANTsREG
<span class="tag fsl">FSL</span><b>fslmaths</b> sanlm_${T1} <span class="opt">-mas</span> ${T1}_brain_mask ${T1}_brain</td>
<td class="io"><span>ANTsBrainExtraction*</span><span>ANTsREG* warps</span><span>*_brain / _mask</span></td>
</tr>
<tr>
<td class="step">QC</td>
<td class="io"><span>*_brain_mask</span><span>${temp}</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>applywarp</b> <span class="opt">--in=</span>${T1}_brain_mask <span class="opt">--ref=</span>${temp} <span class="opt">--warp=</span>transforms/str2std_warp <span class="opt">--interp=</span>nn <span class="opt">--out=</span>qc_bet_in_template</td>
<td class="io"><span>qc_bet_in_template</span></td>
</tr>
</tbody>
</table>
</section>
<!-- ============================ PRECON_2 ============================ -->
<section class="module">
<div class="band">
<span class="mtitle">surfing_safari.sh -r precon_2</span>
<span class="mdesc">Denoise → N4 → segmentation, then hands off to the precon_3 fill/surface steps.</span>
</div>
<table>
<thead><tr>
<th class="c-step">Step / flag</th><th class="c-in">Input</th><th class="c-cmd">Command line</th><th class="c-out">Output</th>
</tr></thead>
<tbody>
<tr class="sub-band"><td colspan="4">intensity prep (top-level driver)<span class="loc">bin/surfing_safari.sh</span></td></tr>
<tr>
<td class="step">denoise</td>
<td class="io"><span>${brain}</span></td>
<td class="cmd"><span class="tag ants">ANTS</span><b>DenoiseImage</b> <span class="opt">-d</span> 3 <span class="opt">-i</span> ${brain} <span class="opt">-o</span> sanlm_${brain} <span class="opt">-v</span> 1</td>
<td class="io"><span>sanlm_${brain}</span></td>
</tr>
<tr>
<td class="step">N4 bias</td>
<td class="io"><span>sanlm_${brain}</span></td>
<td class="cmd"><span class="tag ants">ANTS</span><b>N4BiasFieldCorrection</b> <span class="opt">-d</span> 3 <span class="opt">-i</span> sanlm_${brain} <span class="opt">-c</span> [100x100x100x100,1e-10] <span class="opt">-b</span> [200] <span class="opt">-o</span> sanlm_..._0N4.nii.gz <span class="opt">--verbose</span> 0</td>
<td class="io"><span>sanlm_*_0N4.nii.gz</span></td>
</tr>
<tr class="sub-band"><td colspan="4">seg_animal.sh — tissue segmentation (<span class="muted">-s</span> = ANTs Atropos; else FSL FAST; <span class="muted">-p</span> = priors)<span class="loc">bin/seg_animal.sh</span></td></tr>
<tr>
<td class="step">std→str init</td>
<td class="io"><span>${animal}_brain</span><span>${T1}</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>flirt</b> <span class="opt">-in</span> standards/${animal}/${animal}_brain <span class="opt">-ref</span> ${T1} <span class="opt">-omat</span> seg/std2str.mat <span class="opt">-searchrx/ry/rz</span> -180 180
<span class="tag fsl">FSL</span><b>convert_xfm</b> <span class="opt">-omat</span> transforms/str2std.mat <span class="opt">-inverse</span> transforms/std2str.mat</td>
<td class="io"><span>std2str.mat</span><span>str2std.mat</span></td>
</tr>
<tr>
<td class="step">priors→native</td>
<td class="io"><span>priors/{csf,gm,wm}</span><span>std2str_warp</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>applywarp</b> <span class="opt">-i</span> ${priors}/csf|gm|wm <span class="opt">-r</span> ${T1} <span class="opt">-w</span> transforms/std2str_warp <span class="opt">-o</span> seg/priors1|2|3.nii.gz <span class="muted">(when priors present; SyN path also builds warp via lta_convert → ConvertTransformFile → antsRegistrationSyN.sh)</span></td>
<td class="io"><span>seg/priors{1,2,3}</span></td>
</tr>
<tr>
<td class="step">segment <span class="muted">[FAST]</span></td>
<td class="io"><span>${T1}</span><span>str2std.mat, priors (opt)</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>fast</b> <span class="opt">-B</span> <span class="opt">-n</span> 3 <span class="opt">-o</span> seg/seg ${T1} <span class="muted">— or with priors:</span>
<span class="tag fsl">FSL</span><b>fast</b> <span class="opt">-B -v -n</span> 3 <span class="opt">-a</span> transforms/std2str.mat <span class="opt">-A</span> csf gm wm <span class="opt">-o</span> seg/seg ${T1}
<span class="tag fsl">FSL</span><b>fslmaths</b> seg/seg_pve_2 <span class="opt">-thr</span> ${thresh} <span class="opt">-bin</span> mri/wm_orig</td>
<td class="io"><span>seg/seg_pve_*</span><span>mri/wm_orig</span></td>
</tr>
<tr>
<td class="step">segment <span class="muted">[Atropos]</span></td>
<td class="io"><span>${T1}</span><span>seg/seg_mask</span><span>priors (opt)</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>fslmaths</b> ${mask} <span class="opt">-bin</span> seg/seg_mask.nii.gz
<span class="tag ants">ANTS</span><b>antsAtroposN4.sh</b> <span class="opt">-d</span> 3 <span class="opt">-x</span> seg/seg_mask <span class="opt">-a</span> ${T1} <span class="opt">-c</span> 3 <span class="opt">-o</span> seg/ [<span class="opt">-p</span> seg/priors%d.nii.gz] <span class="opt">-w</span> 0.25|0.5
<span class="tag fsl">FSL</span><b>fslmaths</b> seg/SegmentationPosteriors3 <span class="opt">-thr</span> ${thresh} <span class="opt">-bin</span> mri/wm_orig</td>
<td class="io"><span>seg/Segmentation*</span><span>mri/wm_orig</span></td>
</tr>
</tbody>
</table>
<p class="note">After segmentation, <code>precon_2</code> continues into the <strong>precon_3</strong> fill → tessellate → surface → label → ribbon steps below, then optional <strong>precon_4</strong> downsampling.</p>
</section>
<!-- ============================ PRECON_3 ============================ -->
<section class="module">
<div class="band">
<span class="mtitle">surfing_safari.sh -r precon_3</span>
<span class="mdesc">WM fill & surface generation (assumes segmentation exists). <code>-L</code>/<code>-R</code> = single hemisphere.</span>
</div>
<table>
<thead><tr>
<th class="c-step">Step / flag</th><th class="c-in">Input</th><th class="c-cmd">Command line</th><th class="c-out">Output</th>
</tr></thead>
<tbody>
<!-- fill_animal -->
<tr class="sub-band"><td colspan="4">fill_animal.sh — isometric conform, WM fill, build FreeSurfer volumes<span class="loc">bin/fill_animal.sh</span></td></tr>
<tr>
<td class="step">isometrize</td>
<td class="io"><span>${img} (pixdims)</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>fslinfo</b> ${img} <span class="muted">→ pixdim1/2/3</span>
<span class="tag fsl">FSL</span><b>flirt</b> <span class="opt">-in</span> ${img} <span class="opt">-ref</span> ${img} <span class="opt">-out</span> ${img} <span class="opt">-applyisoxfm</span> ${max} <span class="opt">-interp</span> nearestneighbour <span class="opt">-noresampblur</span> <span class="opt">-omat</span> transforms/isometrize.mat
<span class="tag fsl">FSL</span><b>convert_xfm</b> <span class="opt">-omat</span> transforms/inverse_iso.mat <span class="opt">-inverse</span> isometrize.mat
<span class="tag fsl">FSL</span><b>convert_xfm</b> <span class="opt">-omat</span> str2std_iso.mat <span class="opt">-concat</span> str2std.mat inverse_iso.mat</td>
<td class="io"><span>isometrize.mat</span><span>inverse_iso.mat</span><span>str2std_iso.mat</span></td>
</tr>
<tr>
<td class="step">talairach stubs</td>
<td class="io"><span>brain.nii.gz</span><span>ident.mat / str2std.mat</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>lta_convert</b> <span class="opt">--infsl</span> ident.mat <span class="opt">--outlta</span> transforms/talairach.lta <span class="opt">--src</span> brain <span class="opt">--trg</span> brain
<span class="tag fs">FS</span><b>lta_convert</b> <span class="opt">--infsl</span> ident.mat <span class="opt">--outmni</span> transforms/talairach.xfm <span class="opt">--src</span> brain <span class="opt">--trg</span> brain</td>
<td class="io"><span>talairach.lta</span><span>talairach.xfm</span></td>
</tr>
<tr>
<td class="step">masks→native</td>
<td class="io"><span>${mask} (hem/sub_cort/non_cort)</span><span>std2str.mat</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>flirt</b> <span class="opt">-in</span> ${mask} <span class="opt">-ref</span> ${anat} <span class="opt">-out</span> ${out} <span class="opt">-interp</span> nearestneighbour <span class="opt">-applyxfm -init</span> transforms/std2str.mat
<span class="tag fsl">FSL</span><b>fslmaths</b> ${out} <span class="opt">-thr</span> 0.3 <span class="opt">-bin</span> ${out}</td>
<td class="io"><span>native masks</span></td>
</tr>
<tr>
<td class="step">WM fill / intensity</td>
<td class="io"><span>rawavg</span><span>${wm_seg}</span><span>sub_cort, hem masks</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>fslstats</b> rawavg <span class="opt">-R</span> <span class="muted">(intensity ceiling)</span>
<span class="tag fsl">FSL</span><b>fslmaths</b> rawavg <span class="opt">-div</span> $upper <span class="opt">-mul</span> 150 nu <span class="opt">-odt</span> int
<span class="tag fsl">FSL</span><b>fslmaths</b> chains build: nu_wm, wm+SC, wm_110(+SC), brain, brainmask, sub_cort250, wm, wm_pre_fill (<span class="opt">-fillh</span>), wm_${hemi} (<span class="opt">-mul</span> 255/127), filled
<span class="tag fsl">FSL</span><b>imrm</b> brain_rm_sc</td>
<td class="io"><span>wm, filled</span><span>brain, brainmask</span><span>*_brain (per-hemi)</span></td>
</tr>
<tr>
<td class="step">to FS volumes</td>
<td class="io"><span>*.nii.gz volumes</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mri_convert</b> {left|right}_brain → ?h.brain.finalsurfs.mgz
<span class="tag fs">FS</span><b>mri_convert</b> brain/brainmask/wm/filled/wm_orig/T1/nu/orig → *.mgz
<span class="tag fs">FS</span><b>mri_mask</b> <span class="opt">-T</span> 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
<span class="tag fs">FS</span><b>mri_pretess</b> filled.mgz 255 T1.mgz filled-pretess255.mgz
<span class="tag fs">FS</span><b>mri_pretess</b> filled.mgz 127 T1.mgz filled-pretess127.mgz</td>
<td class="io"><span>*.mgz volumes</span><span>filled-pretess{255,127}.mgz</span></td>
</tr>
<!-- tess_animal -->
<tr class="sub-band"><td colspan="4">tess_animal.sh — tessellation, topology fix, white/pial, curvature, sphere (per hemi)<span class="loc">bin/tess_animal.sh</span></td></tr>
<tr>
<td class="step">prep</td>
<td class="io"><span>brain.mgz, brainmask.mgz</span><span>gm_mask</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mri_mask</b> <span class="opt">-T</span> 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
<span class="tag fs">FS</span><b>mri_convert</b> brain.finalsurfs.mgz brain.finalsurfs.nii.gz
<span class="tag fsl">FSL</span><b>fslstats</b> brain.finalsurfs.nii.gz <span class="opt">-k</span> gm_mask <span class="opt">-P</span> ${grey_pct} <span class="muted">→ min_gray</span></td>
<td class="io"><span>brain.finalsurfs.*</span><span>min_gray</span></td>
</tr>
<tr>
<td class="step">tessellate</td>
<td class="io"><span>filled-pretess{255,127}.mgz</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mri_tessellate</b> filled-pretess255.mgz 255 lh.orig.nofix
<span class="tag fs">FS</span><b>mri_tessellate</b> filled-pretess127.mgz 127 rh.orig.nofix
<span class="tag fs">FS</span><b>mris_info</b> ?h.orig.nofix <span class="muted">→ num vertices</span></td>
<td class="io"><span>?h.orig.nofix</span></td>
</tr>
<tr>
<td class="step">decimate <span class="muted">(if huge)</span></td>
<td class="io"><span>?h.orig.nofix</span></td>
<td class="cmd"><span class="tag wb">WB</span><b>wb_command</b> <span class="opt">-surface-create-sphere</span> 150000 Sphere.150k.R.surf.gii
<span class="tag fs">FS</span><b>mris_smooth</b> <span class="opt">-nw</span> … ; <span class="tag fs">FS</span><b>mris_inflate</b> <span class="opt">-n</span> 30 <span class="opt">-no-save-sulc</span> … ; <span class="tag fs">FS</span><b>mris_sphere</b> <span class="opt">-q -seed</span> 1234 …
<span class="tag fs">FS</span><b>mris_convert</b> ↔ <span class="tag wb">WB</span><b>wb_command</b> <span class="opt">-surface-resample</span> … BARYCENTRIC …</td>
<td class="io"><span>decimated ?h.orig.nofix</span></td>
</tr>
<tr>
<td class="step">smooth1 / inflate1 / qsphere</td>
<td class="io"><span>?h.orig.nofix</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_extract_main_component</b> ?h.orig.nofix ?h.orig.nofix
<span class="tag fs">FS</span><b>mris_smooth</b> <span class="opt">-nw</span> ?h.orig.nofix ?h.smoothwm.nofix
<span class="tag fs">FS</span><b>mris_inflate</b> <span class="opt">-n</span> 1000 <span class="opt">-no-save-sulc</span> ?h.smoothwm.nofix ?h.inflated.nofix
<span class="tag fs">FS</span><b>mris_sphere</b> <span class="opt">-q -seed</span> 1234 ?h.inflated.nofix ?h.qsphere.nofix</td>
<td class="io"><span>?h.smoothwm.nofix</span><span>?h.inflated.nofix</span><span>?h.qsphere.nofix</span></td>
</tr>
<tr>
<td class="step">fix topology</td>
<td class="io"><span>?h.qsphere.nofix</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_fix_topology</b> <span class="opt">-mgz -sphere</span> qsphere.nofix <span class="opt">-ga -seed</span> 1234 <subj> ?h
<span class="tag fs">FS</span><b>mris_euler_number</b> ?h.orig
<span class="tag fs">FS</span><b>mris_remove_intersection</b> ?h.orig ?h.orig</td>
<td class="io"><span>?h.orig</span></td>
</tr>
<tr>
<td class="step">white / pial</td>
<td class="io"><span>?h.brain.finalsurfs</span><span>?h.orig, min_gray (opt)</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_make_surfaces</b> <span class="opt">-noaseg -noaparc -mgz</span> [<span class="opt">-min_gray_at_csf_border</span> ${min_gray}] <span class="opt">-T1</span> ?h.brain.finalsurfs <subj> ?h</td>
<td class="io"><span>?h.white, ?h.pial</span><span>?h.curv, ?h.area, ?h.thickness</span></td>
</tr>
<tr>
<td class="step">smooth2 / inflate2 / curv</td>
<td class="io"><span>?h.white</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_smooth</b> <span class="opt">-n</span> 3 <span class="opt">-nw -seed</span> 1234 ?h.white ?h.smoothwm
<span class="tag fs">FS</span><b>mris_inflate</b> <span class="opt">-dist</span> .01 <span class="opt">-f</span> .001 <span class="opt">-n</span> ${infla} ?h.smoothwm ?h.inflated
<span class="tag fs">FS</span><b>mris_curvature</b> <span class="opt">-thresh</span> .999 <span class="opt">-n -a</span> 5 <span class="opt">-w -distances</span> 10 10 ?h.inflated
<span class="tag fs">FS</span><b>mris_curvature_stats</b> <span class="opt">-m --writeCurvatureFiles -G -o</span> ?h.curv.stats <span class="opt">-F</span> smoothwm <subj> ?h curv sulc</td>
<td class="io"><span>?h.smoothwm, ?h.inflated</span><span>?h.inflated.H/K</span><span>?h.curv.stats</span></td>
</tr>
<tr>
<td class="step">sphere / metrics / midthickness</td>
<td class="io"><span>?h.inflated</span><span>?h.area(.pial), ?h.thickness</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_sphere</b> ?h.inflated ?h.sphere
<span class="tag fs">FS</span><b>mris_calc</b> <span class="opt">-o</span> ?h.area.mid ?h.area add ?h.area.pial · div 2 · <span class="opt">-o</span> ?h.volume ?h.area.mid mul ?h.thickness
<span class="tag fs">FS</span><b>mris_expand</b> <span class="opt">-thickness</span> ?h.white 0.5 ?h.graymid
<span class="tag fs">FS</span><b>mris_convert</b> <span class="opt">--to-scanner</span> ?h.<surf> ?h.<surf>.surf.gii ; <span class="tag fs">FS</span><b>mris_convert</b> ?h.sphere ?h.sphere.surf.gii
<span class="tag wb">WB</span><b>wb_command</b> <span class="opt">-surface-average</span> ?h.midthickness.surf.gii <span class="opt">-surf</span> ?h.white.surf.gii <span class="opt">-surf</span> ?h.pial.surf.gii</td>
<td class="io"><span>?h.sphere</span><span>?h.area.mid, ?h.volume</span><span>?h.graymid, *.surf.gii</span><span>?h.midthickness.surf.gii</span></td>
</tr>
<!-- cortex_labelgen -->
<tr class="sub-band"><td colspan="4">cortex_labelgen.sh — ribbon → cortex/subcortex labels → annotation<span class="loc">bin/cortex_labelgen.sh</span></td></tr>
<tr>
<td class="step">orient probe</td>
<td class="io"><span>brain.mgz</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mri_info</b> brain.mgz <span class="muted">→ determinant, Orientation</span>
<span class="tag fs">FS</span><b>mri_convert</b> mri/brain.mgz mri/aseg.mgz <span class="opt">--out_orientation</span> ${work_orient}</td>
<td class="io"><span>reoriented aseg.mgz</span></td>
</tr>
<tr>
<td class="step">ribbon</td>
<td class="io"><span><subj> surfaces</span><span>sub_cort</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_volmask</b> <span class="opt">--save_ribbon</span> ${subj}
<span class="tag fs">FS</span><b>mri_convert</b> mri/ribbon.mgz mri/ribbon.nii.gz [<span class="opt">--out_orientation</span> …]
<span class="tag fsl">FSL</span><b>fslmaths</b> ribbon <span class="opt">-bin -sub</span> sub_cort <span class="opt">-bin</span> ?h.ribbon (or <span class="opt">-mas / -uthr 21 / -thr 21</span> split)</td>
<td class="io"><span>ribbon.mgz/.nii.gz</span><span>?h.ribbon.nii.gz</span></td>
</tr>
<tr>
<td class="step">vol→surf labels</td>
<td class="io"><span>?h.ribbon</span><span>brain.mgz</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mri_vol2label</b> <span class="opt">--i</span> ?h.ribbon <span class="opt">--id</span> 1 <span class="opt">--v</span> ?h.ribbon <span class="opt">--l</span> ?h.cort.label
<span class="tag fs">FS</span><b>mri_label2vol</b> <span class="opt">--label</span> ?h.cort.label <span class="opt">--temp</span> brain.mgz <span class="opt">--o</span> ?h.cort_vol.mgz <span class="opt">--identity</span>
<span class="tag fs">FS</span><b>mri_vol2surf</b> <span class="opt">--mov</span> ?h.cort_vol.mgz <span class="opt">--ref</span> brain.mgz <span class="opt">--hemi</span> ?h <span class="opt">--o</span> ?h.cort_srf.mgh <span class="opt">--regheader</span> ${subj}
<span class="tag fs">FS</span><b>mri_vol2label</b> <span class="opt">--i</span> ?h.cort_srf.mgh <span class="opt">--id</span> 1|0 <span class="opt">--surf</span> ${subj} ?h <span class="opt">--l</span> label/?h.cortex|subcortex</td>
<td class="io"><span>label/?h.cortex</span><span>label/?h.subcortex</span></td>
</tr>
<tr>
<td class="step">annotate</td>
<td class="io"><span>?h.cortex.label</span><span>cort.annot.ctab</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_label2annot</b> <span class="opt">--s</span> ${subj} <span class="opt">--h</span> ?h <span class="opt">--ctab</span> standards/cort.annot.ctab <span class="opt">--l</span> ?h.Unknown.label <span class="opt">--l</span> ?h.cortex.label <span class="opt">--surf</span> white <span class="opt">--a</span> Cortex</td>
<td class="io"><span>?h.Cortex.annot</span></td>
</tr>
<!-- ribbon at driver level -->
<tr class="sub-band"><td colspan="4">driver — whole-brain ribbon (fake aseg = brain.mgz)<span class="loc">bin/surfing_safari.sh</span></td></tr>
<tr>
<td class="step">cortribbon</td>
<td class="io"><span>?h.white, ?h.pial</span><span>aseg.mgz (=brain.mgz)</span></td>
<td class="cmd"><span class="muted">cp brain.mgz aseg.mgz</span>
<span class="tag fs">FS</span><b>mris_volmask</b> <span class="opt">--save_ribbon</span> $(basename ${brain_dir})</td>
<td class="io"><span>ribbon.mgz</span></td>
</tr>
</tbody>
</table>
</section>
<!-- ============================ PRECON_4 ============================ -->
<section class="module">
<div class="band">
<span class="mtitle">surfing_safari.sh -r precon_4</span>
<span class="mdesc">Downsample native surfaces to an icosphere in HCP space. <code>-v <nverts></code> mandatory. Also runs at the end of precon_2/3 when <code>-v</code> is given.</span>
</div>
<table>
<thead><tr>
<th class="c-step">Step / flag</th><th class="c-in">Input</th><th class="c-cmd">Command line</th><th class="c-out">Output</th>
</tr></thead>
<tbody>
<tr class="sub-band"><td colspan="4">down_surf.sh (per hemi)<span class="loc">bin/down_surf.sh</span></td></tr>
<tr>
<td class="step">build sphere</td>
<td class="io"><span>${verts}</span></td>
<td class="cmd"><span class="tag wb">WB</span><b>wb_command</b> <span class="opt">-surface-create-sphere</span> ${verts} ?h.sphere_${rd}.surf.gii
<span class="tag wb">WB</span><b>wb_command</b> <span class="opt">-surface-flip-lr</span> ?h.sphere_${rd}.surf.gii ?h.sphere_${rd}.flip.surf.gii
<span class="tag wb">WB</span><b>wb_command</b> <span class="opt">-set-structure</span> ?h.sphere_${rd}.surf.gii CORTEX_LEFT|CORTEX_RIGHT</td>
<td class="io"><span>?h.sphere_${rd}.surf.gii</span></td>
</tr>
<tr>
<td class="step">resample</td>
<td class="io"><span>?h.<srf>.surf.gii</span><span>?h.sphere.surf.gii</span></td>
<td class="cmd"><span class="tag wb">WB</span><b>wb_command</b> <span class="opt">-surface-resample</span> ?h.<srf>.surf.gii ?h.sphere.surf.gii ?h.sphere_${rd}.surf.gii BARYCENTRIC ?h.<srf>.surf.gii</td>
<td class="io"><span>downsampled ?h.<srf>.surf.gii</span></td>
</tr>
</tbody>
</table>
</section>
<!-- ============================ PRECON_ART ============================ -->
<section class="module">
<div class="band">
<span class="mtitle">surfing_safari.sh -r precon_art</span>
<span class="mdesc">Visualization-only: STL export incl. cerebellum / non-cortical structures. Run after precon_2. Not for statistics.</span>
</div>
<table>
<thead><tr>
<th class="c-step">Step / flag</th><th class="c-in">Input</th><th class="c-cmd">Command line</th><th class="c-out">Output</th>
</tr></thead>
<tbody>
<tr class="sub-band"><td colspan="4">art.sh<span class="loc">bin/art.sh</span></td></tr>
<tr>
<td class="step">cerebellar masks</td>
<td class="io"><span>non_cort, seg_pve_1</span><span>wm_orig, hem masks</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>imcp</b> seg/seg_pve_1 mri/gray · <span class="tag fsl">FSL</span><b>flirt</b> <span class="opt">-applyisoxfm</span> ${dimNC} → mri/gray
<span class="tag fsl">FSL</span><b>fslmaths</b> build cb_gray / cb_white, L/R split (<span class="opt">-thr -bin -mas -add</span>)</td>
<td class="io"><span>{L,R}_cb_{gray,white}</span></td>
</tr>
<tr>
<td class="step">tessellate + smooth</td>
<td class="io"><span>{L,R}_cb_{gray,white}.nii.gz</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mri_tessellate</b> {L,R}_cb_{gray,white} 1 ?h.cb_{gray,white}
<span class="tag fs">FS</span><b>mris_extract_main_component</b> ${i} ${i}
<span class="tag fs">FS</span><b>mris_smooth</b> <span class="opt">-nw -n</span> 3|6 ${i} ${i}</td>
<td class="io"><span>?h.cb_{gray,white}</span></td>
</tr>
<tr>
<td class="step">export STL</td>
<td class="io"><span>?h.{pial,white}.art.gii</span><span>?h.cb_{gray,white}.gii</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_convert</b> ${i} ${i}.gii · ${i} ${i}.stl
<span class="tag fs">FS</span><b>mris_convert</b> <span class="opt">--combinesurfs</span> ?h.{pial|white}.art.gii ?h.cb_{gray|white}.gii ?h.{full|Wfull}.stl</td>
<td class="io"><span>?h.full.stl</span><span>?h.Wfull.stl</span></td>
</tr>
</tbody>
</table>
</section>
<!-- ============================ UTILS ============================ -->
<section class="module">
<div class="band">
<span class="mtitle">utils/ & group_scripts/</span>
<span class="mdesc">Standalone helpers & group/template tools — not part of the single-subject <code>surfing_safari.sh</code> flow.</span>
</div>
<table>
<thead><tr>
<th class="c-step">Script</th><th class="c-in">Purpose</th><th class="c-cmd">Key command line(s)</th><th class="c-out">Output</th>
</tr></thead>
<tbody>
<tr>
<td class="step">register_surfaces.sh</td>
<td class="io"><span>subject surfaces</span><span>template .tif</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_euler_number</b> …
<span class="tag fs">FS</span><b>mris_register</b> [<span class="opt">-norot</span>][<span class="opt">-reverse</span>] ?h.sphere <template> ?h.<regname>
<span class="tag fs">FS</span><b>mri_surf2surf</b> <span class="opt">--srcsubject --trgsubject --hemi --surfreg --sval --tval --sfmt/--tfmt</span> curv
<span class="tag fs">FS</span><b>mri_label2label</b> <span class="opt">--regmethod</span> surface <span class="opt">--srcsurfreg/--trgsurfreg</span></td>
<td class="io"><span>?h.<regname></span><span>resampled metrics/labels</span></td>
</tr>
<tr>
<td class="step">make_surftemp.sh<br>average_surface_maker.sh</td>
<td class="io"><span>cohort of subjects</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mris_make_template</b> [<span class="opt">-norot</span>] ?h sphere.reg <subjs> ?h.tif
<span class="tag fs">FS</span><b>mris_make_average_surface</b> <span class="opt">-nonorm -i -o -sdir-out</span>
<span class="tag fs">FS</span><b>mris_preproc</b> <span class="opt">--out --f --target --hemi --meas --srcsurfreg</span>
<span class="tag fs">FS</span><b>mri_concat</b> <span class="opt">--mean/--std</span> · <b>mri_surf2surf</b> · <b>mri_add_xform_to_header</b> <span class="opt">-c auto</span> · <b>mri_average</b> <span class="opt">-noconform</span></td>
<td class="io"><span>?h.template.tif</span><span>group average surfaces / maps</span></td>
</tr>
<tr>
<td class="step">consensus_label.sh<br>calc_label_dice.sh</td>
<td class="io"><span>curvature / labels</span></td>
<td class="cmd"><span class="tag fs">FS</span><b>mri_binarize</b> <span class="opt">--i --match</span> 0 [<span class="opt">--inv</span>] <span class="opt">--o</span>
<span class="tag fs">FS</span><b>mri_cor2label</b> <span class="opt">--i --surf</span> <subj> ?h <surf> <span class="opt">--id</span> 1 <span class="opt">--l</span>
<span class="tag fs">FS</span><b>mris_compute_parc_overlap</b> <span class="opt">--s --hemi --label1 --label2</span> <span class="muted">(Dice)</span></td>
<td class="io"><span>consensus labels</span><span>Dice score</span></td>
</tr>
<tr>
<td class="step">intensity_afni_unifize.sh<br>IntensityNormalizeHeadImage.sh</td>
<td class="io"><span>head / brain image</span></td>
<td class="cmd"><span class="tag afni">AFNI</span><b>3dUnifize</b> [<span class="opt">-overwrite</span>] <span class="opt">-input</span> <in> <span class="opt">-prefix</span> <out> [<span class="opt">-ssave</span> scale]
<span class="tag fsl">FSL</span><b>fslmaths</b> <span class="opt">-mas / -div / -mul</span> … ; <span class="tag ants">ANTS</span><b>antsRegistrationSyN.sh</b> (re-register after unifize)</td>
<td class="io"><span>unifized image</span></td>
</tr>
<tr>
<td class="step">manual_bet_fix.sh<br>register_brain_extracted_volume.sh</td>
<td class="io"><span>manually fixed mask</span><span>template</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>flirt</b> <span class="opt">-searchr* -omat</span> manual_fix.mat · <span class="tag fs">FS</span><b>lta_convert</b> <span class="opt">--infsl … --outitk</span>
<span class="tag ants">ANTS</span><b>ConvertTransformFile</b> <span class="opt">--convertToAffineType</span> · <span class="tag fsl">FSL</span><b>fnirt</b> / <span class="tag ants">ANTS</span><b>antsRegistrationSyN.sh</b> <span class="opt">-i</span> init</td>
<td class="io"><span>corrected str2std / std2str warps</span></td>
</tr>
<tr>
<td class="step">ants_to_fsl_warp.sh</td>
<td class="io"><span>ANTs warp + affine</span><span>REF, MOVING</span></td>
<td class="cmd"><span class="tag ants">ANTS</span><b>ImageMath</b> 3 warp_{x,y,z} ExtractVectorComponent <warp> 0|1|2
<span class="tag fsl">FSL</span><b>fslmaths</b> <span class="opt">-mul</span> -1 (flip y[,x]) · <b>fslmerge</b> <span class="opt">-t</span> ants_warp_fsl
<span class="tag ants">ANTS</span><b>ConvertTransformFile</b> 3 <affine> ants_affine_ras.mat <span class="opt">--hm --ras</span>
<span class="tag fs">FS</span><b>lta_convert</b> <span class="opt">--initk … --outfsl</span> · <span class="tag fsl">FSL</span><b>convertwarp</b> <span class="opt">--premat --warp1 --rel --out</span> · <b>invwarp</b> · <b>applywarp</b></td>
<td class="io"><span>str2std_warp.nii.gz</span><span>std2str_warp.nii.gz</span><span>FSL(Inverse)Warped</span></td>
</tr>
<tr>
<td class="step">wm_regional_dual_threshold.sh</td>
<td class="io"><span>std region mask</span><span>wm_seg, rawavg mask</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>applywarp</b> <span class="opt">--interp=</span>nn std_region_mask → native · <span class="tag fsl">FSL</span><b>fslmaths</b> <span class="opt">-dilM / -sub / -mas / -thr / -bin</span> dual-threshold WM → wm_hand_edit</td>
<td class="io"><span>mri/wm_hand_edit</span></td>
</tr>
<tr>
<td class="step">bedpostdir2faket1.sh</td>
<td class="io"><span>completed bedpostX dir</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>fslmaths</b> mean_f1samples <span class="opt">-sqr</span> f1_sqr · mean_f2samples <span class="opt">-sqr</span> f2_sqr · f1_sqr <span class="opt">-add</span> f2_sqr <span class="opt">-sqrt</span> ${prefix}</td>
<td class="io"><span>fake-T1 (anisotropy)</span></td>
</tr>
<tr>
<td class="step">pet_sounds.sh</td>
<td class="io"><span>PET/aux image + ref</span></td>
<td class="cmd"><span class="tag fsl">FSL</span><b>flirt</b> <span class="opt">-dof</span> 12 <span class="opt">-searchr*</span> -180 180 <span class="opt">-omat</span> talairach.mat · <span class="tag fs">FS</span><b>lta_convert</b> <span class="opt">--infsl … --outlta / --outmni</span></td>
<td class="io"><span>talairach.{mat,lta,xfm}</span></td>
</tr>
</tbody>
</table>
</section>
<div class="foot">
<p><strong>QC (out-of-band):</strong> <code>bin/precon_qc.sh</code> drives <span class="tag fsl" style="font-size:10px">FSL</span> <code>fsleyes render</code> (lightbox & 3D scenes: <code>--scene</code>, <code>--zaxis</code>, <code>--numSlices</code>, <code>--overlayType volume|mask|mesh</code>, <code>--outline --outlineWidth</code>) plus ImageMagick <code>montage</code> for tiling. Not a reconstruction step.</p>
<p><strong>Notes.</strong> <span class="tag ants" style="font-size:10px">ANTS</span> <code>Atropos</code> runs inside the <code>antsAtroposN4.sh</code> wrapper (the bare word elsewhere is echoed help text). <code>antsApplyTransforms</code> appears only in a commented validation example in <code>ants_to_fsl_warp.sh</code>. <code>bedpostx</code> / <code>probtrackx</code> / <code>run_first_all</code> are referenced conceptually but never invoked. The <code>precon_alldockerfile</code> installs FreeSurfer 6+, FSL 6+, ANTs 2.3.5+, Workbench 1.5.0+ but issues no processing calls.</p>
<p class="muted">Generated from a static read of the repo at <code>github.com/neurabenn/precon_all</code>. Command lines are condensed for the table; see the per-step source file/line for the verbatim invocation and full option strings.</p>
</div>
</div>
</body>
</html>